Limits...
RNA synthesis by in vitro selected ribozymes for recreating an RNA world.

Martin LL, Unrau PJ, Müller UF - Life (Basel) (2015)

Bottom Line: The RNA world hypothesis states that during an early stage of life, RNA molecules functioned as genome and as the only genome-encoded catalyst.This hypothesis is supported by several lines of evidence, one of which is the in vitro selection of catalytic RNAs (ribozymes) in the laboratory for a wide range of reactions that might have been used by RNA world organisms.These ribozyme classes catalyze nucleoside synthesis, triphosphorylation, and the polymerization of nucleoside triphosphates.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada. lyssam@sfu.ca.

ABSTRACT
The RNA world hypothesis states that during an early stage of life, RNA molecules functioned as genome and as the only genome-encoded catalyst. This hypothesis is supported by several lines of evidence, one of which is the in vitro selection of catalytic RNAs (ribozymes) in the laboratory for a wide range of reactions that might have been used by RNA world organisms. This review focuses on three types of ribozymes that could have been involved in the synthesis of RNA, the core activity in the self-replication of RNA world organisms. These ribozyme classes catalyze nucleoside synthesis, triphosphorylation, and the polymerization of nucleoside triphosphates. The strengths and weaknesses regarding each ribozyme's possible function in a self-replicating RNA network are described, together with the obstacles that need to be overcome before an RNA world organism can be generated in the laboratory.

No MeSH data available.


Related in: MedlinePlus

Two alternative routes to RNA polymerization in an RNA World. (A) RNA polymerization could have proceeded in a fashion analogous to modern DNA or RNA synthesis, where nucleoside triphosphates are first formed, then react with the primer 3'-hydroxyl groups to elongate the primers in 5'- to 3'-direction; (B) Alternatively, RNA World organisms could have relied on RNA polymerization in the 3'- to 5'-direction: here the primer 5'-hydroxyl group is first triphosphorylated, then the activated primer reacts with a nucleoside 3'-hydroxyl group to extend the primer in 3'- to 5'-direction. Note that the monomer in (A) carries three negative charges whereas it is uncharged in (B), facilitating stronger binding of the nucleoside to the elongating primer 5'-terminus.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4390851&req=5

life-05-00247-f005: Two alternative routes to RNA polymerization in an RNA World. (A) RNA polymerization could have proceeded in a fashion analogous to modern DNA or RNA synthesis, where nucleoside triphosphates are first formed, then react with the primer 3'-hydroxyl groups to elongate the primers in 5'- to 3'-direction; (B) Alternatively, RNA World organisms could have relied on RNA polymerization in the 3'- to 5'-direction: here the primer 5'-hydroxyl group is first triphosphorylated, then the activated primer reacts with a nucleoside 3'-hydroxyl group to extend the primer in 3'- to 5'-direction. Note that the monomer in (A) carries three negative charges whereas it is uncharged in (B), facilitating stronger binding of the nucleoside to the elongating primer 5'-terminus.

Mentions: Six of the isolated triphosphorylation ribozymes were tested for their ability to triphosphorylate free nucleosides, instead of RNA oligomers [40]. None of them showed activity for the triphosphorylation of free nucleosides (14C-labeled guanosine). However, the triphosphorylation of free nucleosides may not have been necessary for an RNA world organism: Only if RNA polymerization proceeds in 5'- to 3'-direction is it necessary to triphosphorylate free nucleosides (Figure 5A). If one allows for the idea to polymerize in 3'- to 5'-direction [76,77] then the triphosphorylation of an RNA primer by a ribozyme would prepare the 5'-terminus for the addition of a free nucleoside. Polymerization in 3'- to 5'-direction would then occur by the alternating triphosphorylation of the RNA 5'-terminus and the addition of a nucleoside (Figure 5B). This mechanism has not been observed in today’s life forms; in today’s biology it is probably more beneficial to utilize nucleoside triphosphates and thereby proceed in 5'-3'-direction because nucleoside triphosphates are also used as energy currency to power a large diversity of metabolic reactions. In contrast, the simpler metabolism in the earliest RNA world organisms would have made freely diffusing energy equivalents less beneficial and placed a higher reward on efficient RNA polymerization. In the RNA world, RNA polymerization without nucleoside triphosphates could even have had an advantage: Nucleoside triphosphates carry several negative charges, which cause charge-charge repulsion with the templating RNA strand. In contrast, non-phosphorylated nucleosides do not carry negative charges, mediating stronger binding of the monomer to the growing primer strand [78]. In today’s DNA/RNA/protein life forms the negative charges can be easily shielded by a protein’s positively charged residues, but in an RNA world such shielding would have been more difficult because RNA does not contain positive charges at physiological pH. RNA polymerization in 3'-5'-direction with alternating RNA triphosphorylation and nucleoside addition would have avoided this problem.


RNA synthesis by in vitro selected ribozymes for recreating an RNA world.

Martin LL, Unrau PJ, Müller UF - Life (Basel) (2015)

Two alternative routes to RNA polymerization in an RNA World. (A) RNA polymerization could have proceeded in a fashion analogous to modern DNA or RNA synthesis, where nucleoside triphosphates are first formed, then react with the primer 3'-hydroxyl groups to elongate the primers in 5'- to 3'-direction; (B) Alternatively, RNA World organisms could have relied on RNA polymerization in the 3'- to 5'-direction: here the primer 5'-hydroxyl group is first triphosphorylated, then the activated primer reacts with a nucleoside 3'-hydroxyl group to extend the primer in 3'- to 5'-direction. Note that the monomer in (A) carries three negative charges whereas it is uncharged in (B), facilitating stronger binding of the nucleoside to the elongating primer 5'-terminus.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4390851&req=5

life-05-00247-f005: Two alternative routes to RNA polymerization in an RNA World. (A) RNA polymerization could have proceeded in a fashion analogous to modern DNA or RNA synthesis, where nucleoside triphosphates are first formed, then react with the primer 3'-hydroxyl groups to elongate the primers in 5'- to 3'-direction; (B) Alternatively, RNA World organisms could have relied on RNA polymerization in the 3'- to 5'-direction: here the primer 5'-hydroxyl group is first triphosphorylated, then the activated primer reacts with a nucleoside 3'-hydroxyl group to extend the primer in 3'- to 5'-direction. Note that the monomer in (A) carries three negative charges whereas it is uncharged in (B), facilitating stronger binding of the nucleoside to the elongating primer 5'-terminus.
Mentions: Six of the isolated triphosphorylation ribozymes were tested for their ability to triphosphorylate free nucleosides, instead of RNA oligomers [40]. None of them showed activity for the triphosphorylation of free nucleosides (14C-labeled guanosine). However, the triphosphorylation of free nucleosides may not have been necessary for an RNA world organism: Only if RNA polymerization proceeds in 5'- to 3'-direction is it necessary to triphosphorylate free nucleosides (Figure 5A). If one allows for the idea to polymerize in 3'- to 5'-direction [76,77] then the triphosphorylation of an RNA primer by a ribozyme would prepare the 5'-terminus for the addition of a free nucleoside. Polymerization in 3'- to 5'-direction would then occur by the alternating triphosphorylation of the RNA 5'-terminus and the addition of a nucleoside (Figure 5B). This mechanism has not been observed in today’s life forms; in today’s biology it is probably more beneficial to utilize nucleoside triphosphates and thereby proceed in 5'-3'-direction because nucleoside triphosphates are also used as energy currency to power a large diversity of metabolic reactions. In contrast, the simpler metabolism in the earliest RNA world organisms would have made freely diffusing energy equivalents less beneficial and placed a higher reward on efficient RNA polymerization. In the RNA world, RNA polymerization without nucleoside triphosphates could even have had an advantage: Nucleoside triphosphates carry several negative charges, which cause charge-charge repulsion with the templating RNA strand. In contrast, non-phosphorylated nucleosides do not carry negative charges, mediating stronger binding of the monomer to the growing primer strand [78]. In today’s DNA/RNA/protein life forms the negative charges can be easily shielded by a protein’s positively charged residues, but in an RNA world such shielding would have been more difficult because RNA does not contain positive charges at physiological pH. RNA polymerization in 3'-5'-direction with alternating RNA triphosphorylation and nucleoside addition would have avoided this problem.

Bottom Line: The RNA world hypothesis states that during an early stage of life, RNA molecules functioned as genome and as the only genome-encoded catalyst.This hypothesis is supported by several lines of evidence, one of which is the in vitro selection of catalytic RNAs (ribozymes) in the laboratory for a wide range of reactions that might have been used by RNA world organisms.These ribozyme classes catalyze nucleoside synthesis, triphosphorylation, and the polymerization of nucleoside triphosphates.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada. lyssam@sfu.ca.

ABSTRACT
The RNA world hypothesis states that during an early stage of life, RNA molecules functioned as genome and as the only genome-encoded catalyst. This hypothesis is supported by several lines of evidence, one of which is the in vitro selection of catalytic RNAs (ribozymes) in the laboratory for a wide range of reactions that might have been used by RNA world organisms. This review focuses on three types of ribozymes that could have been involved in the synthesis of RNA, the core activity in the self-replication of RNA world organisms. These ribozyme classes catalyze nucleoside synthesis, triphosphorylation, and the polymerization of nucleoside triphosphates. The strengths and weaknesses regarding each ribozyme's possible function in a self-replicating RNA network are described, together with the obstacles that need to be overcome before an RNA world organism can be generated in the laboratory.

No MeSH data available.


Related in: MedlinePlus